Publications
Publications
Supporting the scientific spirit of transparency, the Stowers Institute for Medical Research makes the data underlying its scientific publications freely accessible to the scientific community. Access to original, unprocessed data allows other scientists to validate and extend findings made by Stowers researchers.
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Drosophila poised enhancers are generated during tissue patterning with the help of repression
Koenecke N, Johnston J, He Q, Meier S, Zeitlinger J. Genome Res. 2017;27:64-74.
Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis
Koenecke N, Johnston J, Gaertner B, Natarajan M, Zeitlinger J. Genome Biol. 2016;17:196.
Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation.
Sun Y, Nien CY, Chen K, Liu HY, Johnston J, Zeitlinger J, Rushlow C. Genome Res. 2015;25:1703-14.
Pharmacologically blocking p53-dependent apoptosis protects intestinal stem cells and mice from radiation.
Wang X, Wei L, Cramer JM, Leibowitz BJ, Judge C, Epperly M, Greenberger J, Wang F, Li L, Stelzner MG, Dunn JC, Martin MG, Lagasse E, Zhang L, Yu J. Sci Rep. 2015;5:8566. doi: 8510.1038/srep08566.
ChIP-nexus enables improved detection of in vivo transcription factor binding footprints.
He Q, Johnston J, Zeitlinger J. Nat Biotechnol. 2015;33:395-401.
Megakaryocytes maintain homeostatic quiescence and promote post-injury regeneration of hematopoietic stem cells.
Zhao M, Perry JM, Marshall H, Venkatraman A, Qian P, He XC, Ahamed J, Li L. Nat Med. 2014;20:1321-1326.
Leucine-rich Repeat-containing G-protein-coupled Receptor 5 Marks Short-term Hematopoietic Stem and Progenitor Cells during Mouse Embryonic Development.
Liu D, He XC, Qian P, Barker N, Trainor PA, Clevers H, Liu H, Li L. J Biol Chem. 2014;289:23809-23816.
TRF2, but not TBP, mediates the transcription of ribosomal protein genes.
Wang YL, Duttke SH, Chen K, Johnston J, Kassavetis GA, Zeitlinger J, Kadonaga JT. Genes Dev. 2014;28:1550-1555.
Leukemia Propagating Cells Rebuild an Evolving Niche in Response to Therapy.
Duan CW, Shi J, Chen J, Wang B, Yu YH, Qin X, Zhou XC, Cai YJ, Li ZQ, Zhang F, Yin MZ, Tao Y, Mi JQ, Li LH, Enver T, Chen GQ, Hong DL. Cancer Cell. 2014;25:778-793.
Enteric bacterial protein AvrA promotes colonic tumorigenesis and activates colonic beta-catenin signaling pathway.
Lu R, Wu S, Zhang YG, Xia Y, Liu X, Zheng Y, Chen H, Schaefer KL, Zhou Z, Bissonnette M, Li L, Sun J. Oncogenesis. 2014;3:e105.
Inhibition of Notch signaling reduces the number of surviving Dclk1+ reserve crypt epithelial stem cells following radiation injury.
Qu D, May R, Sureban SM, Weygant N, Chandrakesan P, Ali N, Li L, Barrett T, Houchen CW. Am J Physiol Gastrointest Liver Physiol. 2014;306:G404-411.
Brief report: Dclk1 deletion in tuft cells results in impaired epithelial repair after radiation injury.
May R, Qu D, Weygant N, Chandrakesan P, Ali N, Lightfoot SA, Li L, Sureban SM, Houchen CW. Stem Cells. 2014;32:822-827.
Molecular Evolution of the Yap/Yorkie Proto-oncogene and Elucidation of its Core Transcriptional Program.
Ikmi A, Gaertner B, Seidel C, Srivastava M, Zeitlinger J, Gibson MC. Mol Biol Evol. 2014;31:1375-1390.
Intestinal subepithelial myofibroblasts support the growth of intestinal epithelial stem cells.
Lei NY, Jabaji Z, Wang J, Joshi VS, Brinkley GJ, Khalil H, Wang F, Jaroszewicz A, Pellegrini M, Li L, Lewis M, Stelzner M, Dunn JC, Martin MG. PLoS One. 2014;9:e84651.
Identification of transcription factor binding sites from ChIP-seq data at high resolution.
Bardet AF, Steinmann J, Bafna S, Knoblich JA, Zeitlinger J, Stark A. Bioinformatics. 2013;29:2705-2713.
A global change in RNA polymerase II pausing during the Drosophila midblastula transition.
Chen K, Johnston J, Shao W, Meier S, Staber C, Zeitlinger J. eLife. 2013;2:e00861. doi: 00810.07554/eLife.00861.
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Isolation and characterization of intestinal stem cells based on surface marker combinations and colony-formation assay.
Wang F, Scoville D, He XC, Mahe MM, Box A, Perry JM, Smith NR, Lei NY, Davies PS, Fuller MK, Haug JS, McClain M, Gracz AD, Ding S, Stelzner M, Dunn JC, Magness ST, Wong MH, Martin MG, Helmrath M, Li L. Gastroenterology. 2013;145:383-395 e321.
Poised RNA Polymerase II Changes over Developmental Time and Prepares Genes for Future Expression.
Gaertner B, Johnston J, Chen K, Wallaschek N, Paulson A, Garruss AS, Gaudenz K, De Kumar B, Krumlauf R, Zeitlinger J. Cell Rep. 2012;2:1670-1683.
Radiofrequency ablation for dysplasia in Barrett's esophagus restores beta-catenin activation within esophageal progenitor cells.
Krishnan K, Komanduri S, Cluley J, Dirisina R, Sinh P, Ko JZ, Li L, Katzman RB, Barrett TA. Dig Dis Sci. 2012;57:294-302.
Noncanonical wnt signaling maintains hematopoietic stem cells in the niche.
Sugimura R, He XC, Venkatraman A, Arai F, Box A, Semerad C, Haug JS, Peng L, Zhong XB, Suda T, Li L. Cell. 2012;150:351-365.
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Emerging questions in transcriptional regulation : What are the sequence rules driving gene regulation?
Nora EP, Aerts S, Wittkopp PJ, Bussemaker HJ, Bulyk M, Sinha S, Zeitlinger J, Crocker J, Fuxman Bass JI. Cell Syst. 2023;14:247-251.
Off the deep end: What can deep learning do for the gene expression field?
Raicu AM, Fay JC, Rohner N, Zeitlinger J, Arnosti DN. J Biol Chem. 2023;299:102760.
Seven myths of how transcription factors read the cis-regulatory code
Zeitlinger J. Curr Opin Syst Biol. 2020;23:22-31.
Cori meets Dobzhansky: Evolution and Gene Expression in St. Louis.
Arnosti DN, Fay JC, Zeitlinger J. A report on the "Evolution and Core Processes in Gene Regulation" meeting in St. Louis, June 25-28, 2015. BioEssays. 2015;37:1042-1044.
Osteoblast ablation burns out functional stem cells.
Zhao M, Li L. Blood. 2015;125:2590-2591.
A high-throughput platform for stem cell niche co-cultures and downstream gene expression analysis.
Gracz AD, Williamson IA, Roche KC, Johnston MJ, Wang F, Wang Y, Attayek PJ, Balowski J, Liu XF, Laurenza RJ, Gaynor LT, Sims CE, Galanko JA, Li L, Allbritton NL, Magness ST. Nat Cell Biol. 2015;17:340-349.
Homing and migration assays of hematopoietic stem/progenitor cells.
He XC, Li Z, Sugimura R, Ross J, Zhao M, Li L. Methods Mol Biol. 2014;1185:279-284.
RNA polymerase II pausing during development.
Gaertner B, Zeitlinger J. Development. 2014;141:1179-1183.
Paused Pol II coordinates tissue morphogenesis in the Drosophila embryo.
Lagha M, Bothma JP, Esposito E, Ng S, Stefanik L, Tsui C, Johnston J, Chen K, Gilmour DS, Zeitlinger J, Levine MS. Cell. 2013;153:976-987.
To be or not to be a stem cell: dissection of cellular and molecular components of haematopoietic stem cell niches.
Perry JM, Li L. EMBO J. 2012;31:1060-1061.
MAPing the role of Kras mutations in hyperplastic polyps.
Barrett T, Li L. Gastroenterology. 2011;141:799-801.
Bone Metastasis Targets The Endosteal Hematopoietic Stem Cell Niche.
Sugimura R, Li L. IBMS BoneKEy. 2011;8:381-384.
Book review of Evolution, Development, and the Predictable Genome by David L. Stern.
Zeitlinger J. Am J Hum Biol. 2011;43:414-420.
Noncanonical Wnt signaling in vertebrate development, stem cells, and diseases.
Sugimura R, Li L. Birth Defects Res C Embryo Today. 2010;90:243-256.
Fountain of Youth: aged blood-forming stem cells could be rejuvenated by young microenvironment.
Yin T, Li L. Cell Res. 2010;20:504-505.
Shifting in balance between osteogenesis and adipogenesis substantially influences hematopoiesis.
Sugimura R, Li L. J Mol Cell Biol. 2010;2:61-62.
Functional assays for hematopoietic stem cell self-renewal.
Perry JM, Li L. Methods Mol Biol. 2010;636:45-54.
Developmental gene regulation in the era of genomics.
Zeitlinger J, Stark A. Dev Biol. 2010;339:230-239.
HSC mobilization: new incites and insights.
Ross J, Li L. Blood. 2009;114:1283-1284.
Visualize eHPCs in different zones.
Yin T, Xie Y, Li L. Blood. 2009;114:230-231.
